But what happens if a unit has both Lunge and Mercy? Assuming they also have other commands there (say, Rescue, Trade, maybe Steal), how much can the box hold before it's too much? Is there even a limit?

In order to make the new skills save with each unit, you had to expand the character RAM I would assume? Are there any other free bytes available in the new unit RAM for new weapon levels? The macros you wrote for the stat pages make it really easy to add in new weapon types to them, so I wanted to try my hand at getting a working version of http://feuniverse.us/t/fe8-arbitrary-number-of-weapon-types/753 so that there can at least be a wind/thunder/fire magic split. Something like this would require two extra bytes, but I've never done any RAM expansion hacking, so I don't know how hard it would be to incorporate the extra weapon types/bytes, and if they're already there that could save some time.

Though maybe I'm getting too far ahead of myself since I still haven't started to work on the other skills I wanted to add...

I didn't expand the character RAM actually, instead I saved them in the area where B/W/L numbers are stored. I left the actual BWL numbers alone, and replaced the hidden "favouritism" stat which tracks how many times you've viewed/selected a unit.

Because only characters up to 0x46 can have BWL data, characters above that do not have room to save their skills. Instead, they look up the skill list to see what skills they should know at their current level. Since these units are mostly generics or at least enemies they don't need to account for branching promos or using items or anything like that.